AIMC Topic: Exons

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CADD-Splice-improving genome-wide variant effect prediction using deep learning-derived splice scores.

Genome medicine Feb 22, 2021
BACKGROUND: Splicing of genomic exons into mRNAs is a critical prerequisite for the accurate synthesis of human proteins. Genetic variants impacting splicing underlie a substantial proportion of genetic disease, but are challenging to identify beyond...
Base Sequence Introns RNA Splicing Exons Humans Deep Learning Genome-Wide Association Study Genetic Variation
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Machine learning based CRISPR gRNA design for therapeutic exon skipping.

PLoS computational biology Jan 8, 2021
Restoring gene function by the induced skipping of deleterious exons has been shown to be effective for treating genetic disorders. However, many of the clinically successful therapies for exon skipping are transient oligonucleotide-based treatments ...
Gene Library Exons Embryonic Stem Cells RNA, Guide, CRISPR-Cas Systems CRISPR-Cas Systems Gene Editing Genetic Therapy Machine Learning Humans Cells, Cultured Animals Mice
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A network-based computational framework to predict and differentiate functions for gene isoforms using exon-level expression data.

Methods (San Diego, Calif.) Jun 10, 2020
MOTIVATION: Alternative splicing makes significant contributions to functional diversity of transcripts and proteins. Many alternatively spliced gene isoforms have been shown to perform specific biological functions under different contexts. In addit...
Protein Isoforms Exons Alternative Splicing Computational Biology Sequence Analysis, RNA High-Throughput Nucleotide Sequencing Gene Expression Regulation Humans Neural Networks, Computer Software
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Exon level machine learning analyses elucidate novel candidate miRNA targets in an avian model of fetal alcohol spectrum disorder.

PLoS computational biology Apr 11, 2019
Gestational alcohol exposure causes fetal alcohol spectrum disorder (FASD) and is a prominent cause of neurodevelopmental disability. Whole transcriptome sequencing (RNA-Seq) offer insights into mechanisms underlying FASD, but gene-level analysis pro...
Big Data Computational Biology Chick Embryo Ethanol Female Animals Gene Expression Profiling Principal Component Analysis Databases, Nucleic Acid Exons Fetal Alcohol Spectrum Disorders Disease Models, Animal Cluster Analysis MicroRNAs Unsupervised Machine Learning Humans Pregnancy
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Deep-learning augmented RNA-seq analysis of transcript splicing.

Nature methods Mar 25, 2019
A major limitation of RNA sequencing (RNA-seq) analysis of alternative splicing is its reliance on high sequencing coverage. We report DARTS (https://github.com/Xinglab/DARTS), a computational framework that integrates deep-learning-based predictions...
Gene Expression Regulation K562 Cells RNA Splicing Exons Alternative Splicing Bayes Theorem Signal Processing, Computer-Assisted RNA High-Throughput Nucleotide Sequencing Epigenomics Hep G2 Cells Models, Statistical Humans Algorithms Reproducibility of Results Gene Expression Profiling Deep Learning Sequence Analysis, RNA
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Discerning novel splice junctions derived from RNA-seq alignment: a deep learning approach.

BMC genomics Dec 27, 2018
BACKGROUND: Exon splicing is a regulated cellular process in the transcription of protein-coding genes. Technological advancements and cost reductions in RNA sequencing have made quantitative and qualitative assessments of the transcriptome both poss...
RNA Splicing Exons Deep Learning Humans Sequence Analysis, RNA Genome, Human Software Sequence Alignment Gene Expression Profiling
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Identification of 170 New Long Noncoding RNAs in .

BioMed research international Jul 11, 2018
Long noncoding RNAs (lncRNAs) are transcripts generally longer than 200 nucleotides with no or poor protein coding potential, and most of their functions are also poorly characterized. Recently, an increasing number of studies have shown that lncRNAs...
Gene Expression Profiling Mice RNA, Long Noncoding Gene Ontology Genome Humans Exons Schistosoma mansoni Female Animals Male
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Improved ontology for eukaryotic single-exon coding sequences in biological databases.

Database : the journal of biological databases and curation Jan 1, 2018
Efficient extraction of knowledge from biological data requires the development of structured vocabularies to unambiguously define biological terms. This paper proposes descriptions and definitions to disambiguate the term 'single-exon gene'. Eukaryo...
Eukaryota Exons Open Reading Frames Databases, Genetic Base Sequence Protein Isoforms Gene Ontology
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Predicting human splicing branchpoints by combining sequence-derived features and multi-label learning methods.

BMC bioinformatics Dec 1, 2017
BACKGROUND: Alternative splicing is the critical process in a single gene coding, which removes introns and joins exons, and splicing branchpoints are indicators for the alternative splicing. Wet experiments have identified a great number of human sp...
Computational Biology Base Sequence Genome, Human Nucleotide Motifs Humans Introns RNA Splicing Machine Learning Exons Position-Specific Scoring Matrices
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Characterization and machine learning prediction of allele-specific DNA methylation.

Genomics Sep 25, 2015
A large collection of Single Nucleotide Polymorphisms (SNPs) has been identified in the human genome. Currently, the epigenetic influences of SNPs on their neighboring CpG sites remain elusive. A growing body of evidence suggests that locus-specific ...
Exons Epigenomics Animals DNA Methylation Mice CpG Islands Humans Polymorphism, Single Nucleotide Alleles Species Specificity Machine Learning Logistic Models Promoter Regions, Genetic Brain Binding Sites
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